Structure of PDB 4dto Chain A Binding Site BS03
Receptor Information
>4dto Chain A (length=903) Species:
12353
(Escherichia phage RB69) [
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MKEFYLTVEQIGDSIFERYIDSNGRERTREVEYKPSLFAHCPESQATKYF
DIYGKPCTRKLFANMRDASQWIKRMEDIGLEALGMDDFKLAYLSDTYNYE
IKYDHTKIRVANFDIEVTSPDGFPEPSQAKHPIDAITHYDSIDDRFYVFD
LLNSPYGNVEEWSIEIAAKLQEQGGDEVPSEIIDKIIYMPFDNEKELLME
YLNFWQQKTPVILTGWNVESFAIPYVYNRIKNIFGESTAKRLSPHRKTRV
KVIENMYGSREIITLFGISVLDYIDLYKKFSFTNQPSYSLDYISEFELNV
GKLKYDGPISKLRESNHQRYISYNIIAVYRVLQIDAKRQFINLSLDMGYY
AKIQIQSVFSPIKTWDAIIFNSLKEQNKVIPQGRSHPVQPYPGAFVKEPI
PNRYKYVMSFDLTSLYPSIIRQVNISPETIAGTFKVAPLHDYINAVAERP
SDVYSCSPNGMMYYKDRDGVVPTEITKVFNQRKEHKGYMLAAQRNGEIIK
EALHNPNLSVDEPLDVDYRFDFSDEIKEKIKKLSAKSLNEMLFRAQRTEV
AGMTAQINRKALINGLAGALGNVWFRYYDLRNATAITTFGQMALQWIERK
VNEYLNEVCGTEGEAFVLYGDTDSIYVSADKIIDKVGESKFRDTNHWVDF
LDKFARERMEPAIDRGFREMCEYMNNKQHLMFMDREAIAGPPLGSKGIGG
FWTGKKRYALNVWDMEGTRYAEPKLKIMGLETQKSSTPKAVQKALKECIR
RMLQEGEESLQEYFKEFEKEFRQLNYISIASVSSANNIAKYDVGGFPGPK
CPFHIRGILTYNRAIKGNIDAPQVVEGEKVYVLPLREGNPFGDKCIAWPS
GTEITDLIKDDVLHWMDYTVLLEKTFIKPLEGFTSAAKLDYEKKASLFDM
FDF
Ligand information
Ligand ID
DCP
InChI
InChI=1S/C9H16N3O13P3/c10-7-1-2-12(9(14)11-7)8-3-5(13)6(23-8)4-22-27(18,19)25-28(20,21)24-26(15,16)17/h1-2,5-6,8,13H,3-4H2,(H,18,19)(H,20,21)(H2,10,11,14)(H2,15,16,17)/t5-,6+,8+/m0/s1
InChIKey
RGWHQCVHVJXOKC-SHYZEUOFSA-N
SMILES
Software
SMILES
ACDLabs 10.04
O=P(O)(O)OP(=O)(O)OP(=O)(O)OCC2OC(N1C(=O)N=C(N)C=C1)CC2O
OpenEye OEToolkits 1.5.0
C1C(C(OC1N2C=CC(=NC2=O)N)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O
CACTVS 3.341
NC1=NC(=O)N(C=C1)[C@H]2C[C@H](O)[C@@H](CO[P@](O)(=O)O[P@](O)(=O)O[P](O)(O)=O)O2
OpenEye OEToolkits 1.5.0
C1[C@@H]([C@H](O[C@H]1N2C=CC(=NC2=O)N)CO[P@@](=O)(O)O[P@@](=O)(O)OP(=O)(O)O)O
CACTVS 3.341
NC1=NC(=O)N(C=C1)[CH]2C[CH](O)[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)O2
Formula
C9 H16 N3 O13 P3
Name
2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE
ChEMBL
CHEMBL560403
DrugBank
DB03258
ZINC
ZINC000008215945
PDB chain
4dto Chain A Residue 1001 [
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Receptor-Ligand Complex Structure
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PDB
4dto
Contribution of Partial Charge Interactions and Base Stacking to the Efficiency of Primer Extension at and beyond Abasic Sites in DNA.
Resolution
2.05 Å
Binding residue
(original residue number in PDB)
L412 S414 L415 Y416 R482 N564 T622 D623
Binding residue
(residue number reindexed from 1)
L412 S414 L415 Y416 R482 N564 T622 D623
Annotation score
1
Enzymatic activity
Enzyme Commision number
2.7.7.7
: DNA-directed DNA polymerase.
3.1.11.-
Gene Ontology
Molecular Function
GO:0000166
nucleotide binding
GO:0003676
nucleic acid binding
GO:0003677
DNA binding
GO:0003887
DNA-directed DNA polymerase activity
GO:0004527
exonuclease activity
GO:0008408
3'-5' exonuclease activity
GO:0046872
metal ion binding
Biological Process
GO:0006260
DNA replication
GO:0006261
DNA-templated DNA replication
GO:0039686
bidirectional double-stranded viral DNA replication
GO:0039693
viral DNA genome replication
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Molecular Function
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Biological Process
External links
PDB
RCSB:4dto
,
PDBe:4dto
,
PDBj:4dto
PDBsum
4dto
PubMed
22630605
UniProt
Q38087
|DPOL_BPR69 DNA-directed DNA polymerase (Gene Name=43)
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